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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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megahit -> flye reformatting #29

Closed mihinduk closed 3 years ago

mihinduk commented 3 years ago

Hi Scott, This is the current reformat command between megahit and flye:

reformat.sh in={output.rename} out={output.size} \
        ml={config[MINLENGTH]} \
        ow=t \
        -Xmx{config[System][Memory]}g;

If you try to run flye with the same MINLENGTH as megahit, you may fail immediately because of duplicate names. This can be solved by adding this to the reformat command: uniquenames=t

Kathie

shandley commented 3 years ago

I believe this has been fixed in the newest version. If it's still an issue we can revisit.